Reprogramming

This article is about the epigenetic phenomenon. For the writing of computer code, see computer programming.

In biology, reprogramming refers to erasure and remodeling of epigenetic marks, such as DNA methylation, during mammalian development or in cell culture.[1] Such control is also often associated with alternative covalent modifications of histones.

DNA methylation patterns are largely erased and then re-established between generations in mammals. Almost all of the methylations from the parents are erased, first during gametogenesis, and again in early embryogenesis, with demethylation and remethylation occurring each time. Demethylation of early embryogenesis occurs in the preimplantation period in two stages – initially in the zygote, then the first few embryonic replication cycles of morula and blastula. A wave of methylation then takes place during the implantation stage of the embryo, with CpG islands protected from methylation. This results in global repression and allows housekeeping genes to be expressed in all cells. In the post-implantation stage, methylation patterns are stage- and tissue-specific with changes that would define each individual cell type lasting stably over a long time.[2]

After fertilization some cells of the newly formed embryo migrate to the germinal ridge and will eventually become the germ cells (sperm and oocytes). Due to the phenomenon of genomic imprinting, maternal and paternal genomes are differentially marked and must be properly reprogrammed every time they pass through the germline. Therefore, during the process of gametogenesis the primordial germ cells must have their original biparental DNA methylation patterns erased and re-established based on the sex of the transmitting parent.

After fertilization, the paternal and maternal genomes are demethylated in order to erase their epigenetic signatures and acquire totipotency. There is asymmetry at this point: the male pronucleus undergoes a quick and active demethylation meanwhile the female pronucleus is demethylated passively during consecutive cell divisions. Despite of the global nature of this process, there are certain sequences that get to avoid it, as differentially methylated regions (DMRS) associated with imprinted genes, retrotransposons and centromeric heterochromatin. Remethylation is needed again to differentiate the embryo into a complete organism.[3]

In vitro manipulation of pre-implantation embryos has been shown to disrupt methylation patterns at imprinted loci[4] and plays a crucial role in cloned animals.[5]

The first person to successfully demonstrate reprogramming was John Gurdon, who in 1962 demonstrated that differentiated somatic cells could be reprogrammed back into an embryonic state when he managed to obtain swimming tadpoles following the transfer of differentiated intestinal epithelial cells into enucleated frog eggs.[6] For this achievement he received the 2012 Nobel Prize in Medicine alongside Shinya Yamanaka.[7] Yamanaka was the first to demonstrate (in 2006) that this somatic cell nuclear transfer or oocyte-based reprogramming process (see below), that Gurdon discovered, could be recapitulated (in mice) by defined factors (Oct4, Sox2, Klf4, and c-Myc) to generate induced pluripotent stem cells (iPSCs).[8] Other combinations of genes have also been used.[9]

The properties of cells obtained after reprogramming can vary significantly, in particular among iPSCs.[10] Factors leading to variation in the performance of reprogramming and functional features of end products include genetic background, tissue source, reprogramming factor stoichiometry and stressors related to cell culture.[10]

Reprogramming is distinct from development of a somatic epitype,[12] as somatic epitypes can potentially be altered after an organism has left the developmental stage of life.[13] During somatic cell nuclear transfer, the oocyte turns off tissue specific genes in the Somatic cell nucleus and turns back on embryonic specific genes.